[gmx-users] Umberella sampling

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Sun May 8 16:56:24 CEST 2011 

Dear Dr.Justin

Thank you for your complete explanation.
Please let me discribe  where is NPT.cpt  comes from:

Before doing Pulling step,I did an NPT step (as your tutorial) to generate
NPT ensemble.
the outputs of this step were NPT.cpt,  NPT.gro and NPT.enr and ...

Then I used NPT.gro for Pulling step to generate config0.gro and ...

After this step I used the NPT.cpt  and  config0.gro and .... to generate
umbrella0.tpr with  grompp.
I think it is obvious now ,where is  NPT.cpt  come from!

I think my mistake is as you noted.I didn't use any  -t option in
grompp,Then I lost the information for npt ensemble.

What do you think
Thanks in advance for your reply




On Sun, May 8, 2011 at 7:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> I didn't any equilibration for any windows! Because:
>> As I know the thermodynamics of the system had wroten in NPT.cpt file (for
>> example the velocities and etc).
>>
>
> Then where does NPT.cpt come from?  Presumably, if you have this file, you
> did some equilibration.  I don't understand what you've done.  If you want
> to rely on previous, equilibrium dynamics under an NPT ensemble, you must do
> equilibrium MD (not steered) for each configuration under the desired
> conditions, then pass the .cpt file to grompp -t when building the umbrella
> sampling input files.
>
>
>  Then when I use that  in grompp for each windows ,I expect  the same
>> characteristics of system as before(At least the same T)!
>>
>>
> With "gen_vel = no" and no record of the prior state, this is not a
> reasonable expectation.  You will get a temperature based on the initial
> forces present in the system (which determine initial velocities).  The
> resulting temperature may or may not be identical to the previous state, but
> under the influence of a thermostat, you will reach the desired temperature.
>
> If you're attempting to follow my tutorial directly, at this point I think
> you should stop and consider the discussion I have in the tutorial on
> maintaining the ensemble:
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html
>
> In the example system (one I know very well), it was satisfactory to simply
> use
> "gen_vel = no" and allow these initial forces to govern the resulting
> dynamics.  In many other cases (probably most), you should:
>
> 1. Generate your configurations (SMD, etc)
> 2. Run individual NPT simulations (or whatever ensemble) for each desired
> starting configuration (and thus obtain npt0.cpt, npt1.cpt, etc)
> 3. Initiate umbrella sampling windows using the npt*.cpt files from each
> window.
>
> Otherwise, skip step 2, use "gen_vel = yes" and discard the first few
> hundred ps as equilibration in each window.
>
>
>  Actually after PULLING step I used the following commands:
>> grompp  -f  umbrella.mdp   -c   config0.gro  -p  complex.top  -o
>>  umbrella0.tpr  -n index.ndx
>> mdrun  -v  -deffnm  umbrella0    -px  pullx0.xvg   -pf   pullf0.xvg   -cpi
>>   NPT.cpt
>>
>> what is your point of view now?
>>
>
> These commands do not necessarily preserve the ensemble.  Without providing
> suitable information to grompp -t, the initial state is lost.  I still don't
> know where NPT.cpt comes from.  You say you're running grompp immediately
> after pulling, which is a non-equilibrium ensemble that you don't want to
> preserve as input into umbrella sampling.  That, and likely the settings in
> SMD vs. US are different, so if NPT.cpt corresponds to your SMD simulation,
> you probably don't want to be using that for all your umbrella sampling
> windows, as the information it contains is for one single snapshot somewhere
> along the SMD run.  If this is not the case, and you've generated NPT.cpt in
> some other manner, you will have to explain where it came from.
>
>
>  What do you think if I use NPT.enr  OR   NPT.trr   OR   in
>> grompp(especially  NPT.enr) ?
>>
>
> Not necessary.  Using .cpt files is more accurate.
>
>
>  Because all of information about NPT step are included in this files.
>>
>>
> Note entirely.  The differences between using .edr + .trr vs. .cpt alone
> are very small, but using a .cpt file is the most rigorously correct way to
> maintain the ensemble.
>
> -Justin
>
>  Thanks in advance for your
>>
>> On Sun, May 8, 2011 at 5:47 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    mohsen ramezanpour wrote:
>>
>>        Dear Dr.Justin
>>
>>        Regarding doing umbrella sampling:
>>        I used gen_vel =no
>>        and I prefer to use from thermodynamics of system in  NPT.cpt
>>
>>        Although the T and P were as I did set in NPT.mdp file (T=310
>>        ,P=1 bar)
>>        But  their values in my umbrela.log files are not as before (for
>>        example  P=-8.434578e+1)
>>
>>        Where did I wrong?
>>
>>
>>    I have no clue.  You didn't provide your commands or any evidence
>>    that the prior ensemble was to be maintained.  If you have done NPT
>>    equilibration in each window, then pass the .cpt file to grompp and
>>    the ensemble should be preserved in each window.  Note that an
>>    instantaneous pressure value means nothing, as discussed weekly on
>>    this list and online:
>>
>>    http://www.gromacs.org/Documentation/Terminology/Pressure
>>
>>    It is the average that is most meaningful.
>>
>>    -Justin
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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